Publications

evolutionary dynamics of wau-like wolbachia variants in neotropical drosophila spp.	wolbachia bacteria are common intracellular symbionts of arthropods and have been extensively studied in drosophila. most research focuses on two old word hosts, drosophila melanogaster and drosophila simulans, and does not take into account that some of the wolbachia associations in these species may have evolved only after their fast global expansion and after the exposure to wolbachia of previously isolated habitats. here we looked at wolbachia of neotropical drosophila species. seventy-one l ...	2006	16391124
proceedings of the smbe tri-national young investigators' workshop 2005. accurate inference and estimation in population genomics.	both intra- and interspecific genomic comparisons have revealed local similarities in the level and frequency of mutational variation, as well as in patterns of gene expression. this autocorrelation between measurements leads to violations of assumptions of independence in many statistical methods, resulting in misleading and incorrect inferences. here i show that autocorrelation can be due to many factors and is present across the genome. using a one-dimensional spatial stochastic model, i furt ...	2006	16407459
induced paternal effects mimic cytoplasmic incompatibility in drosophila.	wolbachia is an intracellular microbe found in a wide diversity of arthropod and filarial nematode hosts. in arthropods these common bacteria are reproductive parasites that manipulate central elements of their host's reproduction to increase their own maternal transmission in one of several ways. cytoplasmic incompatibility (ci) is one such manipulation where sperm are somehow modified in infected males and this modification must be rescued by the presence of the same bacterial strain in the eg ...	2006	16489228
mobilization of a hobo-related sequence in the genome of drosophila simulans.	the hobo transposable element can occur under three forms in the drosophila genome: as a complete element (also called canonical), as internally deleted copies, or as hobo-related sequences (relics). some evidence indicated that canonical elements and internally deleted copies are recent acquisitions of drosophila genomes, while the "relics" are old components, normally degenerated and immobile. here we present the characterization of a hobo-related sequence, found in the genome of a hypermutabl ...	2006	16502088
contrasted polymorphism patterns in a large sample of populations from the evolutionary genetics model drosophila simulans.	african populations of drosophila simulans are thought to be ancestral in this model species and are increasingly used for testing general hypotheses in evolutionary genetics. it is often assumed that african populations are more likely to be at a neutral mutation drift equilibrium than other populations. here we examine population structuring and the demographic profile in nine populations of d. simulans. we surveyed sequence variation in four x-linked genes (runt, sevenless, sex-lethal, and ve ...	2006	16510794
adaptive protein evolution and regulatory divergence in drosophila.	two recent studies demonstrated a positive correlation between divergence in gene expression and protein sequence in drosophila. this correlation could be driven by positive selection or variation in functional constraint. to distinguish between these alternatives, we compared patterns of molecular evolution for 1,862 genes with two previously reported estimates of expression divergence in drosophila. we found a slight negative trend (nonsignificant) between positive selection on protein sequenc ...	2006	16537654
estimating the genomewide rate of adaptive protein evolution in drosophila.	when polymorphism and divergence data are available for multiple loci, extended forms of the mcdonald-kreitman test can be used to estimate the average proportion of the amino acid divergence due to adaptive evolution--a statistic denoted alpha. but such tests are subject to many biases. most serious is the possibility that high estimates of alpha reflect demographic changes rather than adaptive substitution. testing for between-locus variation in alpha is one possible way of distinguishing betw ...	2006	16582427
competition between drosophila melanogaster and drosophila simulans: ii. the improvement of competitive ability through selection.		1952	16589182
strong purifying selection on the odysseus gene in two clades of sibling species of the drosophila montium species subgroup.	the odysseus (odsh) gene was duplicated from its ancestral neuron-expressed gene, unc-4, and then evolved very rapidly under strong positive darwinian selection as a speciation gene causing hybrid-male sterility between closely related species of the drosophila simulans clade. has odsh also experienced similar positive selection between drosophila sibling species other than those of the simulans clade? we cloned and sequenced odsh and unc-4 from two clades of the drosophila montium species subgr ...	2006	16612548
wolbachia infection suppresses both host defence and parasitoid counter-defence.	endosymbiotic bacteria in the genus wolbachia have been linked to several types of reproductive parasitism, which enhance their own transmission, while their direct effects on the host vary from beneficial to neutral or detrimental. here, we report negative effects of infection on immunity-related traits of drosophila simulans and the parasitoid wasp leptopilina heterotoma. infected d. simulans showed a reduced ability to encapsulate parasitoid eggs, compared to a tetracycline-treated, bacterium ...	2006	16618671
ongoing loss of the tirant transposable element in natural populations of drosophila simulans.	tirant is a long terminal repeat (ltr) retrotransposon with an average of 11 insertion sites on the chromosome arms of drosophila melanogaster flies collected from natural populations worldwide. in the sibling species drosophila simulans, tirant is found only in african populations, which harbor a few insertion sites (1 to 5) on the chromosome arms, although some tirant sequences are present in the heterochromatin of most populations. this distribution in d. simulans reflects either the recent g ...	2006	16626897
wolbachia infection influences the development of culex pipiens embryo in incompatible crosses.	wolbachia are maternally inherited endosymbiotic bacteria that infect many arthropod species and have evolved several different ways for manipulating their host, the most frequent being cytoplasmic incompatibility (ci). ci leads to embryo death in crosses between infected males and uninfected females, as well as in crosses between individuals infected by incompatible wolbachia strains. in the mosquito culex pipiens, previous studies suggested developmental variation in embryos stemming from diff ...	2006	16639421
proteomic identification of drosophila melanogaster male accessory gland proteins, including a pro-cathepsin and a soluble gamma-glutamyl transpeptidase.	in drosophila melanogaster, the male seminal fluid contains proteins that are important for reproductive success. many of these proteins are synthesised by the male accessory glands and are secreted into the accessory gland lumen, where they are stored until required. previous studies on the identification of drosophila accessory gland products have largely focused on characterisation of male-specific accessory gland cdnas from d. melanogaster and, more recently, drosophila simulans. in the pres ...	2006	16670001
genetic architecture of variation in sex-comb tooth number in drosophila simulans.	the sex comb on the forelegs of drosophila males is a secondary sexual trait, and the number of teeth on these combs varies greatly within and between species. to understand the relationship between the intra- and interspecific variation, we performed quantitative trait locus (qtl) analyses of the intraspecific variation in sex-comb tooth number. we used five mapping populations derived from two inbred drosophila simulans strains that were divergent in the number of sex-comb teeth. although no q ...	2006	16709273
origination of an x-linked testes chimeric gene by illegitimate recombination in drosophila.	the formation of chimeric gene structures provides important routes by which novel proteins and functions are introduced into genomes. signatures of these events have been identified in organisms from wide phylogenic distributions. however, the ability to characterize the early phases of these evolutionary processes has been difficult due to the ancient age of the genes or to the limitations of strictly computational approaches. while examples involving retrotransposition exist, our understandin ...	2006	16715176
inbreeding reduces power-law scaling in the distribution of fluctuating asymmetry: an explanation of the basis of developmental instability.	the study of fluctuating asymmetry has been controversial because of conflicting results found in much of the primary literature. it has been suggested that the source of this conflict is the fact that the basis of fluctuating asymmetry is poorly understood and that, as a consequence, methodology of fluctuating asymmetry studies may be flawed. a new model for the phenomenological basis of fluctuating asymmetry, that variation in fluctuating asymmetry is in large part due to the random exponentia ...	2006	16736063
ubiquitous selective constraints in the drosophila genome revealed by a genome-wide interspecies comparison.	non-coding dna comprises approximately 80% of the euchromatic portion of the drosophila melanogaster genome. non-coding sequences are known to contain functionally important elements controlling gene expression, but the proportion of sites that are selectively constrained is still largely unknown. we have compared the complete d. melanogaster and drosophila simulans genome sequences to estimate mean selective constraint (the fraction of mutations that are eliminated by selection) in coding and n ...	2006	16751341
positive selection versus demography: evolutionary inferences based on an unusual haplotype structure in drosophila simulans.	coalescent simulations were used to investigate the possible role of population subdivision and history in shaping nucleotide variation in a recombining 88-kb genomic fragment of drosophila simulans displaying an unusual large-scale haplotype structure. the multilocus analysis, based on summary statistics using specific demographic null models under recombination, indicates that the observed levels of linkage disequilibrium differed significantly from the values expected under different bottlene ...	2006	16757657
body size patterns in drosophila inhabiting a mesocosm: interactive effects of spatial variation in temperature and abundance.	body size is a major component of fitness. however, the relative contributions of different factors to optimal size, and the determinants of spatial and temporal variation in size, have not been fully established empirically. here, we use a mesocosm of a drosophilidae assemblage inhabiting decaying nectarines to investigate the influence of spatial variation in temperature on adult body size in drosophila simulans sturtevant. two treatments were established; one in the sun where developing larva ...	2006	16773332
interspecific transfer of wolbachia into the mosquito disease vector aedes albopictus.	intracellular wolbachia bacteria are obligate, maternally inherited endosymbionts found frequently in insects and other invertebrates. the evolutionary success of wolbachia is due in part to an ability to manipulate reproduction. in mosquitoes and many other insects, wolbachia causes a form of sterility known as cytoplasmic incompatibility (ci). wolbachia-induced ci has attracted interest as a potential agent for affecting medically important disease vectors. however, application of the approach ...	2006	16777718
a wolbachia-associated fitness benefit depends on genetic background in drosophila simulans.	the alpha-proteobacteria wolbachia infect a number of insect species and influence host reproduction to favour the spread of infected females through a population. the fitness effect of this infection is important in understanding the spread and maintenance of wolbachia within and among host populations. however, a full elucidation of fitness effect requires careful control of host genetic background. here, i transferred a single clone of wolbachia (the wha strain) into three genetically distinc ...	2006	16777731
wolbachia infection reduces sperm competitive ability in an insect.	the maternally inherited bacterium wolbachia pipientis imposes significant fitness costs on its hosts. one such cost is decreased sperm production resulting in reduced fertility of male drosophila simulans infected with cytoplasmic incompatibility (ci) inducing wolbachia. we tested the hypothesis that wolbachia infection affects sperm competitive ability and found that wolbachia infection is indeed associated with reduced success in sperm competition in non-virgin males. in the second male role, ...	2006	16777737
intraspecific variation in survival and mitochondrial oxidative phosphorylation in wild-caught drosophila simulans.	lifespans of organisms vary greatly even among individuals of the same species. under the framework of the free oxygen radical theory of aging, it is predicted that variation in individual lifespan within a species will correlate with variation in the accumulation of oxidative damage to cell components from reactive oxygen species. in this study we test the hypothesis that variation in survival of three wild-caught drosophila simulans fly lines (hw09, nc48 and md106) correlates with three key as ...	2006	16842495
sex-ratio meiotic drive in drosophila simulans: cellular mechanism, candidate genes and evolution.	the sex-ratio trait, reported in a dozen drosophila species, is a type of naturally occurring meiotic drive in which the driving elements are located on the x chromosome. typically, as the result of a shortage of y-bearing spermatozoa, males carrying a sex-ratio x chromosome produce a large excess of female offspring. the presence of sex-ratio chromosomes in a species can have considerable evolutionary consequences, because they can affect individual fitness and trigger extended intragenomic con ...	2006	16856861
sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression.	we describe sebida, a database of genes with sex-biased expression. the database integrates results from multiple, independent microarray studies comparing male and female gene expression in drosophila melanogaster, drosophila simulans and anopheles gambiae. sebida uses standard nomenclature, which allows individual genes to be compared across different microarray platforms and to be queried by gene name, symbol, or annotation number. in addition to ratios of male/female expression for each gene ...	2006	16882652
fast protein evolution and germ line expression of a drosophila parental gene and its young retroposed paralog.	this is the first detailed study of the evolution, phylogenetic distribution, and transcription of one young retroposed gene, cg13732, and its parental gene cg15645, whose functions are unknown. cg13732 is a recognizable retroposed copy of cg15645 retaining the signals of this process. we name the parental gene cervantes and the retrogene quijote. to determine when this duplication occurred and the phylogenetic distribution of quijote, we employed polymerase chain reaction, southern blotting, an ...	2006	16916943
intron length evolution in drosophila.	i present data on the evolution of intron lengths among 3 closely related drosophila species, d. melanogaster, drosophila simulans, and drosophila yakuba. using d. yakuba as an outgroup, i mapped insertion and deletion mutations in 148 introns (spanning approximately 30 kb) to the d. melanogaster and d. simulans lineages. intron length evolution in the 2 sister species has been different: in d. melanogaster, x-linked introns have increased slightly in size, whereas autosomal ones have decreased ...	2006	16923822
nora virus, a persistent virus in drosophila, defines a new picorna-like virus family.	several viruses, including picornaviruses, are known to establish persistent infections, but the mechanisms involved are poorly understood. here, a novel picorna-like virus, nora virus, which causes a persistent infection in drosophila melanogaster, is described. it has a single-stranded, positive-sense genomic rna of 11879 nt, followed by a poly(a) tail. unlike other picorna-like viruses, the genome has four open reading frames (orfs). one orf encodes a picornavirus-like cassette of proteins fo ...	2006	16963764
genome-wide patterns of expression in drosophila pure species and hybrid males. ii. examination of multiple-species hybridizations, platforms, and life cycle stages.	species often produce sterile hybrids early in their evolutionary divergence, and some evidence suggests that hybrid sterility may be associated with deviations or disruptions in gene expression. in support of this idea, many studies have shown that a high proportion of male-biased genes are underexpressed, compared with non-sex-biased genes, in sterile f1 male hybrids of drosophila species. in this study, we examined and compared patterns of misexpression in sterile f1 male hybrids of drosophil ...	2007	17032727
maximum likelihood estimation of ancestral codon usage bias parameters in drosophila.	we present a likelihood method for estimating codon usage bias parameters along the lineages of a phylogeny. the method is an extension of the classical codon-based models used for estimating dn/ds ratios along the lineages of a phylogeny. however, we add one extra parameter for each lineage: the selection coefficient for optimal codon usage (s), allowing joint maximum likelihood estimation of s and the dn/ds ratio. we apply the method to previously published data from drosophila melanogaster, d ...	2007	17041152
microsatellite variation and differentiation in african and non-african populations of drosophila simulans.	drosophila simulans originated in sub-saharan africa or madagascar and colonized the rest of the world after the last glaciation about 10 000 years ago. consistent with this demographic history, sub-saharan african populations have been shown to harbour higher levels of microsatellite and sequence variation than cosmopolitan populations. nevertheless, only limited information is available on the population structure of d. simulans. here, we analysed x-linked and autosomal microsatellite loci in ...	2006	17054491
recurrent positive selection at bgcn, a key determinant of germ line differentiation, does not appear to be driven by simple coevolution with its partner protein bam.	surveys of nucleotide sequence polymorphism in drosophila melanogaster and drosophila simulans were performed at 2 interacting loci crucial for gametogenesis: bag-of-marbles (bam) and benign gonial cell neoplasm (bgcn). at the polymorphism level, both loci appear to be evolving under the expectations of the neutral theory. however, ratios of polymorphism and divergence for synonymous and nonsynonymous mutations depart significantly from neutral expectations for both loci consistent with a previo ...	2007	17056645
pervasive adaptive evolution among interactors of the drosophila hybrid inviability gene, nup96.	nup96 is involved in a lethal hybrid incompatibility between 2 fruit fly species, drosophila melanogaster and drosophila simulans. recurrent adaptive evolution drove the rapid functional divergence of nup96 in both the d. melanogaster and the d. simulans lineages. functional divergence of nup96 between these 2 species is unexpected as nup96 encodes part of the nup107 subcomplex, an architectural component of nuclear pore complexes, the macromolecular channels in nuclear envelopes that mediate nu ...	2007	17056646
phylogenetic incongruence in the drosophila melanogaster species group.	drosophila melanogaster and its close relatives are used extensively in comparative biology. despite the importance of phylogenetic information for such studies, relationships between some melanogaster species group members are unclear due to conflicting phylogenetic signals at different loci. in this study, we use twelve nuclear loci (eleven coding and one non-coding) to assess the degree of phylogenetic incongruence in this model system. we focus on two nodes: (1) the node joining the drosophi ...	2007	17071113
lethality in drosophila melanogaster/drosophila simulans species hybrids is not associated with substantial transcriptional misregulation.	the cross of drosophila melanogaster females to drosophila simulans males produces lethal f1 hybrid males. these lethal phenotypes can be suppressed by mutations in the d. melanogaster gene hybrid male rescue (hmr), demonstrating that hmr has a major role in causing lethality in this hybridization. we performed parallel crosses to generate viable (hmr-) and lethal (hmr+) hybrid male larvae and used microarrays to compare whole-genome transcriptional profiles between these two samples. this compa ...	2007	17075830
drosophila flies in "evolution canyon" as a model for incipient sympatric speciation.	the genetic basis of population divergence leading to adaptive radiation and speciation is a major unresolved problem of evolutionary biology. molecular elucidation of "speciation genes" advanced recently, yet it remains without clear identification of the gene complexes participating in reproductive isolation between natural populations, particularly, in sympatry. genetic divergence was discovered between drosophila melanogaster populations inhabiting ecologically contrasting, opposite slopes i ...	2006	17108081
two dobzhansky-muller genes interact to cause hybrid lethality in drosophila.	the dobzhansky-muller model proposes that hybrid incompatibilities are caused by the interaction between genes that have functionally diverged in the respective hybridizing species. here, we show that lethal hybrid rescue (lhr) has functionally diverged in drosophila simulans and interacts with hybrid male rescue (hmr), which has functionally diverged in d. melanogaster, to cause lethality in f1 hybrid males. lhr localizes to heterochromatic regions of the genome and has diverged extensively in ...	2006	17124320
comparative genomic analysis of allatostatin-encoding (ast) genes in drosophila species and prediction of regulatory elements by phylogenetic footprinting.	the role of the yxfgla family of allatostatin (ast) peptides in dipterans is not well-established. the recent completion of sequencing of genomes for multiple drosophila species provides an opportunity to study the evolutionary variation of the allatostatins and to examine regulatory elements that control gene expression. we performed comparative analyses of ast genes from seven drosophila species (drosophila melanogaster, drosophila simulans, drosophila ananassae, drosophila yakuba, drosophila ...	2007	17175069
insertional dna and spontaneous mutation at the white locus in drosophila simulans.	a large body of data on molecular analyses of several multiallelic loci in drosophila melanogaster has demonstrated a high incidence of mobile dna element insertions among spontaneous mutations. in the sibling species d. simulans, the dispersed, middle repetitive, nomadic sequences are reduced to about one-seventh that of its sibling species (dowsett and young 1982). does this reduced amount of middle repetitive dna (or mobile dna sequences) mean that in d. simulans the occurrence of insertion m ...	1987	17186619
symbiotic bacteria in oocyte and ovarian cell mitochondria of the tick ixodes ricinus: biology and phylogenetic position.	under natural conditions, eukaryote cells may contain bacteria. arthropods such as ticks, insects or mites are a group particularly favoured by the obligate intracellular bacteria. while arthropods are vectors for some of them, other bacteria inhabit invertebrate host cells having entered mutualistic interactions. such endosymbionts dwell usually in the host cell vacuoles or cytoplasm but have been also reported from tick oocyte mitochondria. the microorganisms contribute to mitochondria degrada ...	2007	17226040
genetic studies on drosophila simulans. i. introduction. hybrids with drosophila melanogaster.		1920	17245951
genetic studies on drosophila simulans. ii. sex-linked group of genes.		1921	17245955
genetic studies on drosophila simulans. iii. autosomal genes. general discussion.		1921	17245963
a comprehensive study of genic variation in natural populations of drosophila melanogaster. iii. variations in genetic structure and their causes between drosophila melanogaster and its sibling species drosophila simulans.	the natural populations of drosophila melanogaster and drosophila simulans were compared for their genetic structure. a total of 114 gene-protein loci were studied in four mainland (from europe and africa) and an island (seychelle) populations of d. simulans and the results were compared with those obtained on the same set of homologous loci in fifteen worldwide populations of d. melanogaster. the main results are as follows: (1) d. melanogaster shows a significantly higher proportion of loci po ...	1987	17246411
unidirectional incompatibility in drosophila simulans: inheritance, geographic variation and fitness effects.	in california, drosophila simulans females from some populations (type w) produce relatively few adult progeny when crossed to males from some other populations (type r), but the productivity of the reciprocal cross is comparable to within-population controls. these two incompatibility types are widespread in north america and are also present elsewhere. both types sometimes occur in the same population. type r females always produce type r progeny irrespective of the father's type. however, mat ...	1988	17246430
the bristles of hybrids between drosophila melanogaster and drosophila simulans.		1932	17246649
the lack of effect of etherization on the x-ray mutation rate in drosophila simulans.		1935	17246765
cytologic studies on the abnormal development of the eggs of the claret mutant type of drosophila simulans.		1936	17246793
the influence of age and sex of the germ cells on the frequency of mutation in drosophila simulans and drosophila melanogaster.		1937	17246834
the effects of interspecific competition on the dynamics of a polymorphism in an experimental population of drosophila melanogaster.	populations of drosophila melanogaster with a fourth-chromosome polymorphism were subjected to different levels of competition with drosophila simulans. the dynamics of the polymorphism and the equilibrium frequencies of the sparkling allele were seen to depend on the competitive level, while the higher productivity of the competing populations was shown to be due to the initial parental density. the effects of competition on fitness components were quantified by fitting the data to both a two-s ...	1979	17248954
unusual pattern of nucleotide sequence variation at the os-e and os-f genomic regions of drosophila simulans.	nucleotide variation at the genomic region encompassing the odorant-binding protein genes os-e and os-f (os region) was surveyed in two populations of drosophila simulans, one from europe and the other from africa. we found that the european population shows an atypical and large haplotype structure, which extends throughout the approximately 5-kb surveyed genomic region. this structure is depicted by two major haplotype groups segregating at intermediate frequency in the sample, one haplogroup ...	2007	17277360
adaptive genic evolution in the drosophila genomes.	determining the extent of adaptive evolution at the genomic level is central to our understanding of molecular evolution. a suitable observation for this purpose would consist of polymorphic data on a large and unbiased collection of genes from two closely related species, each having a large and stable population. in this study, we sequenced 419 genes from 24 lines of drosophila melanogaster and its close relatives. together with data from drosophila simulans, these data reveal the following. ( ...	2007	17284599
sympatric drosophila simulans flies with distinct mtdna show difference in mitochondrial respiration and electron transport.	the role of mitochondrial dna (mtdna) in mitochondrial metabolism is understudied yet humans harboring specific mtdna types age at dissimilar rates, are unequally susceptible to various diseases, and differentially adapt to various environmental conditions. this study compares mitochondrial respiration, proton leak and electron transport of drosophila simulans males with distinct mtdna haplogroups (siii and -iii) that were collected in sympatry in kenya. despite the large divergence among haplog ...	2007	17296496
rapid evolution of smell and taste receptor genes during host specialization in drosophila sechellia.	our understanding of the genetic basis of host specialization in insects is limited to basic information on the number and location of genetic factors underlying changes in conspicuous phenotypes. we know nothing about general patterns of molecular evolution that may accompany host specialization but are not traceable to a single prominent phenotypic change. here, i describe changes in the entire repertoire of 136 olfactory receptor (or) and gustatory receptor (gr) genes of the recently speciali ...	2007	17360391
a female-biased expressed elongase involved in long-chain hydrocarbon biosynthesis and courtship behavior in drosophila melanogaster.	drosophila melanogaster produces sexually dimorphic cuticular pheromones that are a key component of the courtship behavior leading to copulation. these molecules are hydrocarbons, with lengths of 23 and 25 carbons in males (mainly with one double bond) and 27 and 29 carbons in females (mainly with two double bonds). here, we describe an elongase gene, elof, with female-biased expression. the 771-bp orf encodes a 257-aa protein that shows the highest sequence identity with mouse ssc1 elongase (3 ...	2007	17360514
systems-level analysis and evolution of the phototransduction network in drosophila.	networks of interacting genes are responsible for generating life's complexity and for mediating how organisms respond to their environment. thus, a basic understanding of genetic variation in gene networks in natural populations is important for elucidating how changes at the genetic level map to higher levels of biological organization. here, using the well-characterized phototransduction network in drosophila, we analyze variation in gene expression within and between two closely related spec ...	2007	17360639
adaptive evolution of metabolic pathways in drosophila.	the adaptive significance of enzyme variation has been of central interest in population genetics. yet, how natural selection operates on enzymes in the larger context of biochemical pathways has not been broadly explored. a basic expectation is that natural selection on metabolic phenotypes will target enzymes that control metabolic flux, but how adaptive variation is distributed among enzymes in metabolic networks is poorly understood. here, we use population genetic methods to identify enzyme ...	2007	17379620
organization of foraging behavior in larvae of cosmopolitan, widespread, and endemic drosophila species.	to explore the evolution of higher order behavioral traits we investigated the organization of foraging patterns in first instar larvae of natural populations of drosophila. we examined drosophila simulans (cosmopolitan); d. mauritania (widespread); d. pavani, and d. gaucha (endemic). larvae of these four species share the same behavior components that comprise foraging (locomotion, feeding, bending, and turning). d. simulans and d. mauritania larvae show uncoupled foraging patterns organized in ...	2007	17394057
prevalence of positive selection among nearly neutral amino acid replacements in drosophila.	we have estimated the selective effects of amino acid replacements in natural populations by comparing levels of polymorphism in 91 genes in african populations of drosophila melanogaster with their divergence from drosophila simulans. the genes include about equal numbers whose level of expression in adults is greater in males, greater in females, or approximately equal in the sexes. markov chain monte carlo methods were used to sample key parameters in the stationary distribution of polymorphi ...	2007	17409186
from parasite to mutualist: rapid evolution of wolbachia in natural populations of drosophila.	wolbachia are maternally inherited bacteria that commonly spread through host populations by causing cytoplasmic incompatibility, often expressed as reduced egg hatch when uninfected females mate with infected males. infected females are frequently less fecund as a consequence of wolbachia infection. however, theory predicts that because of maternal transmission, these "parasites" will tend to evolve towards a more mutualistic association with their hosts. drosophila simulans in california provi ...	2007	17439303
comparative population genetics of the immunity gene, relish: is adaptive evolution idiosyncratic?	the frequency of adaptive evolution acting on common loci in distant lineages remains an outstanding question in evolutionary biology. we asked whether the immunity factor, relish, a gene with a history of directional selection in drosophila simulans, shows evidence of a similar selective history in other drosophila species. we found only weak evidence of recurrent adaptive protein evolution at the relish locus in three sister species pairs, suggesting that this key component of the insect immun ...	2007	17505533
new candidate genes for sex-comb divergence between drosophila mauritiana and drosophila simulans.	a large-effect qtl for divergence in sex-comb tooth number between drosophila simulans and d. mauritiana was previously mapped to 73a-84ab. here we identify genes that are likely contributors to this divergence. we first improved the mapping resolution in the 73a-84ab region using 12 introgression lines and 62 recombinant nearly isogenic lines. to further narrow the list of candidate genes, we assayed leg-specific expression and identified genes with transcript-level evolution consistent with a ...	2007	17565959
canalization of segmentation and its evolution in drosophila.	segmentation in drosophila embryogenesis occurs through a hierarchical cascade of regulatory gene expression driven by the establishment of a diffusion-mediated morphogen gradient. here, we investigate the response of this pattern formation process to genetic variation and evolution in egg size. specifically, we ask whether spatial localization of gap genes kruppel (kr) and giant (gt) and the pair-rule gene even-skipped (eve) during cellularization is robust to genetic variation in embryo length ...	2007	17569783
recent ltr retrotransposon insertion contrasts with waves of non-ltr insertion since speciation in drosophila melanogaster.	ltr and non-ltr retrotransposons exhibit distinct patterns of abundance within the drosophila melanogaster genome, yet the causes of these differences remain unknown. here we investigate whether genomic differences between ltr and non-ltr retrotransposons reflect systematic differences in their insertion history. we find that for 17 ltr and 10 non-ltr retrotransposon families that evolve under a pseudogene-like mode of evolution, most elements from ltr families have integrated in the very recent ...	2007	17592135
mitochondrial dna variation is associated with measurable differences in life-history traits and mitochondrial metabolism in drosophila simulans.	recent studies have used a variety of theoretical arguments to show that mitochondrial (mt) dna rarely evolves as a strictly neutral marker and that selection operates on the mtdna of many species. however, the vast majority of researchers are not convinced by these arguments because data linking mtdna variation with phenotypic differences are limited. we investigated sequence variation in the three mtdna and nine nuclear genes (including all isoforms) that encode the 12 subunits of cytochrome c ...	2007	17598752
the drosulfakinin 0 (dsk 0) peptide encoded in the conserved dsk gene affects adult drosophila melanogaster crop contractions.	we report that the drosulfakinin 0 (dsk 0; nqktmsfnh2) structure and genomic organization are conserved. the dsk 0 c-terminus, sfnh2, is widely distributed in the animal kingdom suggesting it defines a novel peptide family. we also report the first description of dsk 0 activity. dsk 0, i (dsk i, fddyghmrfnh2), and ii (dsk ii, ggddqfddyghmrfnh2) are encoded in sulfakinin (dsk). drosophila erecta, drosophila sechellia, drosophila simulans, and drosophila yakuba shared 62.5-87.5% identity to drosop ...	2007	17632121
transepithelial transport of salicylate by the malpighian tubules of insects from different orders.	the organic anion salicylate is a plant secondary metabolite that protects plants against phytophagous insects. in this study, a combination of salicylate-selective microelectrodes and a radioisotope tracer technique was used to study the transepithelial transport of salicylate by the malpighian tubules of 10 species of insects from five orders. our results show that salicylate is transported into the lumen of the malpighian tubules in all the species evaluated, except rhodnius prolixus. the tra ...	2007	17640663
variation in fiber number of a male-specific muscle between drosophila species: a genetic and developmental analysis.	we characterize a newly discovered morphological difference between species of the drosophila melanogaster subgroup. the muscle of lawrence (mol) contains about four to five fibers in d. melanogaster and drosophila simulans and six to seven fibers in drosophila mauritiana and drosophila sechellia. the same number of nuclei per fiber is present in these species but their total number of mol nuclei differs. this suggests that the number of muscle precursor cells has changed during evolution. our c ...	2008	17651361
sympatric drosophila simulans flies with distinct mtdna show age related differences in mitochondrial metabolism.	the primary causes of age-related changes in mitochondrial metabolism are not known. the goal of this study is to document the influence of naturally occurring mtdna variation on age dependent changes in mitochondrial respiration, hydrogen peroxide (h(2)o(2)) generation and antioxidant defenses in the fly drosophila simulans. possible changes include an increase in rates of reactive oxygen species production with age and/or an age dependent decrease in antioxidant response. for this study we hav ...	2007	17681231
effects of wolbachia on sperm maturation and architecture in drosophila simulans riverside.	wolbachia is an intracellular obligate symbiont, that is relatively common in insects and also found in some nematodes. cytoplasmic incompatibility (ci) is the most commonly expressed form, of several sex altering phenotypes caused by this rickettsial-like bacterium. ci is induced when infected males mate with uninfected females, and is likely the result of bacterial-induced modification of sperm grown in a wolbachia-infected environment. several studies have explored the dynamics of wolbachia b ...	2007	17693061
sex differences in survival and mitochondrial bioenergetics during aging in drosophila.	the goal of this study is to test the role of mitochondria and of mitochondrial metabolism in determining the processes that influence aging of female and male drosophila. we observe that drosophila simulans females tended to have shorter lifespan, higher levels of hydrogen peroxide production and significantly lower levels of catalase but not superoxide dismutase compared to males. in contrast, mammalian females tend to be longer lived, have lower rates of reactive oxygen species production and ...	2007	17725690
intersexes in drosophila simulans.		1920	17773838
species-specific positive selection of the male-specific lethal complex that participates in dosage compensation in drosophila.	in many taxa, males and females have unequal ratios of sex chromosomes to autosomes, which has resulted in the invention of diverse mechanisms to equilibrate gene expression between the sexes (dosage compensation). failure to compensate for sex chromosome dosage results in male lethality in drosophila. in drosophila, a male-specific lethal (msl) complex of proteins and noncoding rnas binds to hundreds of sites on the single male x chromosome and up-regulates gene expression. here we use populati ...	2007	17878295
adaptive protein evolution of x-linked and autosomal genes in drosophila: implications for faster-x hypotheses.	patterns of sex chromosome and autosome evolution can be used to elucidate the underlying genetic basis of adaptative change. evolutionary theory predicts that x-linked genes will adapt more rapidly than autosomes if adaptation is limited by the availability of beneficial mutations and if such mutations are recessive. in drosophila, rates of molecular divergence between species appear to be equivalent between autosomes and the x chromosome. however, molecular divergence contrasts are difficult t ...	2007	17884828
working harder to stay alive: metabolic rate increases with age in drosophila simulans but does not correlate with life span.	the hypothesis that metabolic rate is inversely correlated with life span has long been debated. another area of controversy has been the relationship between metabolic rate and aging. in most molecular studies key aspects of cellular metabolism have been shown to decline with age. less attention has been focused on metabolic rate as an organism ages. we studied the survival of three drosophila simulans fly lines and measured whole organism metabolic rate, mitochondrial dna copy number and walki ...	2007	17915248
comparative analysis of mitochondrial genotype and aging.	a common feature across all animals, including humans, is that mitochondrial bioenergetics is linked to oxidative stress, but the nature of these relationships with survival is yet to be properly defined. in this study we included 12 drosophila simulans isofemale lines: four of each distinct mtdna haplogroup (sii, -ii, and -iii). first, we investigated sequence variation in six mtdna and 13 nuclear encoded genes (nine nuclear-encoded subunits, and the four known isoforms, of complex iv of the el ...	2007	17934050
adaptive gene expression divergence inferred from population genomics.	detailed studies of individual genes have shown that gene expression divergence often results from adaptive evolution of regulatory sequence. genome-wide analyses, however, have yet to unite patterns of gene expression with polymorphism and divergence to infer population genetic mechanisms underlying expression evolution. here, we combined genomic expression data--analyzed in a phylogenetic context--with whole genome light-shotgun sequence data from six drosophila simulans lines and reference se ...	2007	17967066
rampant adaptive evolution in regions of proteins with unknown function in drosophila simulans.	adaptive protein evolution is pervasive in drosophila. genomic studies, thus far, have analyzed each protein as a single entity. however, the targets of adaptive events may be localized to particular parts of proteins, such as protein domains or regions involved in protein folding. we compared the population genetic mechanisms driving sequence polymorphism and divergence in defined protein domains and non-domain regions. interestingly, we find that non-domain regions of proteins are more frequen ...	2007	17971876
a sex-ratio meiotic drive system in drosophila simulans. i: an autosomal suppressor.	sex ratio distortion (sex-ratio for short) has been reported in numerous species such as drosophila, where distortion can readily be detected in experimental crosses, but the molecular mechanisms remain elusive. here we characterize an autosomal sex-ratio suppressor from d. simulans that we designate as not much yang (nmy, polytene chromosome position 87f3). nmy suppresses an x-linked sex-ratio distorter, contains a pair of near-perfect inverted repeats of 345 bp, and evidently originated throug ...	2007	17988172
a sex-ratio meiotic drive system in drosophila simulans. ii: an x-linked distorter.	the evolution of heteromorphic sex chromosomes creates a genetic condition favoring the invasion of sex-ratio meiotic drive elements, resulting in the biased transmission of one sex chromosome over the other, in violation of mendel's first law. the molecular mechanisms of sex-ratio meiotic drive may therefore help us to understand the evolutionary forces shaping the meiotic behavior of the sex chromosomes. here we characterize a sex-ratio distorter on the x chromosome (dox) in drosophila simulan ...	2007	17988173
population genomics: whole-genome analysis of polymorphism and divergence in drosophila simulans.	the population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. here we present a population genetic analysis of drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, d. melanogaster and d. yakuba. we discovered previou ...	2007	17988176
rapid r2 retrotransposition leads to the loss of previously inserted copies via large deletions of the rdna locus.	r2 non-long terminal repeat retrotransposable elements insert specifically into the 28s rrna genes of a wide range of animals. these elements maintain long-term stable relationships with the host genome. by scoring the variation present at the 5' ends of individual r2 copies, lines of drosophila simulans have been identified with high rates of r2 retrotransposition. comparing the r2 elements present in the parents with that of their progeny after 1 or 30 generations in this report revealed that ...	2008	18003600
do wolbachia-associated incompatibilities promote polyandry?	the genetic incompatibility avoidance hypothesis as an explanation for the polyandrous mating strategies (mating with more than one male) of females of many species has received significant attention in recent years. it has received support from both empirical studies and a meta-analysis, which concludes that polyandrous females enjoy increased reproductive success through improved offspring viability relative to monandrous females. in this study we investigate whether polyandrous female drosoph ...	2008	18067571
selective sweeps in a 2-locus model for sex-ratio meiotic drive in drosophila simulans.	a way to identify loci subject to positive selection is to detect the signature of selective sweeps in given chromosomal regions. it is revealed by the departure of dna polymorphism patterns from the neutral equilibrium predicted by coalescent theory. we surveyed dna sequence variation in a region formerly identified as causing "sex-ratio" meiotic drive in drosophila simulans. we found evidence that this system evolved by positive selection at 2 neighboring loci, which thus appear to be required ...	2008	18071199
genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in drosophila.	the effect of recurrent selective sweeps is a spatially heterogeneous reduction in neutral polymorphism throughout the genome. the pattern of reduction depends on the selective advantage and recurrence rate of the sweeps. because many adaptive substitutions responsible for these sweeps also contribute to nonsynonymous divergence, the spatial distribution of nonsynonymous divergence also reflects the distribution of adaptive substitutions. thus, the spatial correspondence between neutral polymorp ...	2007	18073425
the structure of the 18s rrna, a molecule that might be evolutionarily related to some receptors of innate immunity.	comparisons between the sequences of insect and vertebrate 18s rrnas and the sequences of mammalian formyl peptide and some vertebrate chemokine receptor mrnas demonstrated non-random structural similarities between these two groups of rnas. it has been proposed that sections of the more ancient and conserved rrna genes could have participated in the building of these more recent genes involved in immune responses. here we analyze the sequence architecture of the 18s rrna in insects (drosophila ...	2007	18075861
tetracycline treatment influences mitochondrial metabolism and mtdna density two generations after treatment in drosophila.	tetracycline is commonly used to clear wolbachia from infected insects. studies then compare specific biochemical and/or life-history traits between infected and uninfected individuals with the same genetic background. we investigated the potential for tetracycline to influence mitochondrial efficiency and mitochondrial (mt)dna density two generations after treatment in drosophila simulans. we observed that antibiotic treatment resulted in a decline in inorganic phosphate incorporated into atp p ...	2007	18093008
the expression of alleles at the cubitus interrupts locus in hybrids between drosophila melanogaster and drosophila simulans.		1949	18131555
the impact of shared ancestral variation on hybrid male lethality--a 16 codon indel in the drosophila simulans lhr gene.	the lethal hybrid rescue (lhr) gene causes hybrid male lethality in crosses between drosophila simulans and d. melanogaster. lhr(2) is a d. simulans allele, which rescues hybrid males. it has been recently proposed that a 16 codon insertion, which distinguishes the d. melanogaster and the canonical d. simulans allele, and is lacking in lhr(2), may be responsible for the functional divergence of d. melanogaster and d. simulans lhr alleles. here, we show that the lhr(2) allele lacking the insertio ...	2008	18194231
evolution of a desaturase involved in female pheromonal cuticular hydrocarbon biosynthesis and courtship behavior in drosophila.	drosophila species exhibit polymorphism in female pheromonal cuticular hydrocarbons, with 7-monoenes produced in drosophila simulans and 7,11-dienes in most populations of drosophila melanogaster (5,9-dienes in several african populations). a female-biased desaturase, desatf, expressed only in d. melanogaster is involved in the synthesis of 7,11-dienes. we investigated the role of desatf in 5,9-diene flies. we constructed a 5,9-diene strain knock-down for desatf and showed that desatf is involve ...	2008	18207084
divergence times in caenorhabditis and drosophila inferred from direct estimates of the neutral mutation rate.	accurate inference of the dates of common ancestry among species forms a central problem in understanding the evolutionary history of organisms. molecular estimates of divergence time rely on the molecular evolutionary prediction that neutral mutations and substitutions occur at the same constant rate in genomes of related species. this underlies the notion of a molecular clock. most implementations of this idea depend on paleontological calibration to infer dates of common ancestry, but taxa wi ...	2008	18234705
a new test for selection applied to codon usage in drosophila simulans and d. mauritiana.	in many organisms, synonymous codon usage is biased by a history of natural selection. however, codon bias, itself, does not indicate that selection is ongoing; it may be a vestige of past selection. simple statistical tests have been devised to infer ongoing selection on codon usage by comparing the derived state frequency spectra at polymorphic sites segregating either derived preferred codons or derived unpreferred codons; if selection is effective, the frequency of derived states should be h ...	2008	18288436
evolution of gene expression in the drosophila olfactory system.	host plant shifts by phytophagous insects play a key role in insect evolution and plant ecology. such shifts often involve major behavioral changes as the insects must acquire an attraction and/or lose the repulsion to the new host plant's odor and taste. the evolution of chemotactic behavior may be due, in part, to gene expression changes in the peripheral sensory system. to test this hypothesis, we compared gene expression in the olfactory organs of drosophila sechellia, a narrow ecological sp ...	2008	18296696
drosophila simulans lethal hybrid rescue mutation (lhr) rescues inviable hybrids by restoring x chromosomal dosage compensation and causes fluctuating asymmetry of development.	the drosophila simulans lhr rescues lethal hybrids from the cross of d. melanogaster and d. simulans. we describe here, the phenotypes of lhr dependent rescue hybrids and demonstrate the effects of lhr on functional morphology of the salivary chromosomes in the hybrids. our results reveal that the phenotypes of the 'lhr dependent rescued' hybrids were largely dependent on the genetic background and the dominance in species and hybrids, and not on lhr. cytological examination reveal that while th ...	2007	18305340
an intron loss of dfak gene in species of the drosophila melanogaster subgroup and phylogenetic analysis.	drosophila focal adhesion kinase (dfak) gene is a single-copy nuclear gene. previous study revealed that drosophila melanogaster and drosophila simulans had lost an intron precisely within the tyrosine kinase (tyk) domain of this gene. however, this did not happen in several other drosophila species, including drosophila elegans, drosophila ficusphila, drosophila biarmipes, drosophila jambulina, drosophila prostipennis, drosophila takahashii, and drosophila pseudoobscura. in the current study, h ...	2009	18310070
a candidate complex approach to study functional mitochondrial dna changes: sequence variation and quaternary structure modeling of drosophila simulans cytochrome c oxidase.	a problem with studying evolutionary dynamics of mitochondrial (mt) dna is that classical population genetic techniques cannot identify selected substitutions because of genetic hitchhiking. we circumvented this problem by employing a candidate complex approach to study sequence variation in cytochrome c oxidase (cox) genes within and among three distinct drosophila simulans mtdna haplogroups. first, we determined sequence variation in complete coding regions for all cox mtdna and nuclear loci a ...	2008	18320260
recurrent tandem gene duplication gave rise to functionally divergent genes in drosophila.	tandem gene duplication is one of the major gene duplication mechanisms in eukaryotes, as illustrated by the prevalence of gene family clusters. tandem duplicated paralogs usually share the same regulatory element, and as a consequence, they are likely to perform similar biological functions. here, we provide an example of a newly evolved tandem duplicate acquiring novel functions, which were driven by positive selection. cg32708, cg32706, and cg6999 are 3 clustered genes residing in the x chrom ...	2008	18408233
multiple rescue factors within a wolbachia strain.	wolbachia-induced cytoplasmic incompatibility (ci) is expressed when infected males are crossed with either uninfected females or females infected with wolbachia of different ci specificity. in diploid insects, ci results in embryonic mortality, apparently due to the the loss of the paternal set of chromosomes, usually during the first mitotic division. the molecular basis of ci has not been determined yet; however, several lines of evidence suggest that wolbachia exhibits two distinct sex-depen ...	2008	18430940
the acylphosphatase (acyp) alleles associate with male hybrid sterility in drosophila.	hybrid defects are believed to result from genetic incompatibilities between genes that have evolved in separate parental lineages. these genetic dysfunctions on the hybrid genomic background, also known as dobzhansky-muller incompatibilities, can be an incipient signature of speciation, and as such - a subject of active research. here we present evidence that acyp locus (cg16870) that encodes acylphosphatase, a small enzyme that catalyzes the hydrolysis of acylphosphates and participates in ion ...	2008	18440166
wolbachia infection alters olfactory-cued locomotion in drosophila spp.	wolbachia pipientis is an endosymbiotic bacterium present in diverse insect species. although it is well studied for its dramatic effects on host reproductive biology, little is known about its effects on other aspects of host biology, despite its presence in a wide array of host tissues. this study examined the effects of three wolbachia strains on two different drosophila species, using a laboratory performance assay for insect locomotion in response to olfactory cues. the results demonstrate ...	2008	18456851